[gmx-users] help with distance restraints

[David Mobley]

I think I answered this a couple days ago, or a very similar question.
Try searching the list.

David


On 8/7/06, Owen, Michael <MichaelOwen at creighton.edu> wrote:
>
>
>
>
> Hello,
>
>  I am trying to use NMR restraints to position a Cu2+ ion around specific
> residues of a peptide.  I added Cu2+ using "genion" and then initiated
> "grompp" before an energy minim minimization.  I received the following
> error message while executing "grompp":
>
>
>  -------------------------------------------------------
>  Program grompp, VERSION 3.3.1
>  Source code file: toppush.c, line: 1108
>
>  Fatal error:
>  [ file "Ab_Cu.top", line 5864 ]:
>               Atom index (67248) in distance_restraints out of bounds (1-1)
>  -------------------------------------------------------
>
>
>  Below is the entry in the topology file.  Line 5864 contains the value 97
> and the value 67248 refers is the atom number of the Cu2+ ion.
>
>
>  [ distance_restraints ]
>
>  ;ai     aj      type    index   type'   low     up1     up2     fac
>  67248   97      1       1       1       0.185   0.195   0.2     1.0
>  67248   196     1       1       1       0.185   0.195   0.2     1.0
>  67248   213     1       1       1       0.185   0.195   0.2     1.0
>  67248   148     1       1       1       0.195   0.205   0.21    1.0
>
>  Could you suggest any changes that would eliminate my error?
>
>  Thanks in advance,
>
>  Michael Owen
>
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